Health officials investigating the national fungal meningitis outbreak caused by tainted steroid injections had thought that the worst was over. The number of new cases was dwindling. Then came patients like Anna Adair.

An avid gardener and dog-breeder, Adair was rolled into a Michigan emergency room in a wheelchair Nov. 15. She had
been bedridden for days, and that morning a bolt of pain in her lower back had caused her to tumble to the bathroom floor.

Doctors quickly reached a disturbing realization: An infection caused by black mold had infiltrated her spine, near where she had received an injection made by a Massachusetts pharmacy, and spread into the bone. It was not the ­meningitis that sickened hundreds of others in late summer and early fall, but part of a frightening second wave of ­fungal infections caused by contaminated drugs.

Dozens more people have now been diagnosed with excruciating abscesses or inflamed nerves in their backs that are proving formidable to cure.

In a health alert issued Thursday, the federal Centers for Disease Control and Prevention said it is worried that some patients with spinal infections may not even be aware of their condition because the symptoms mimic the very back pain they originally sought to treat with steroids. The agency is now recommending that doctors consider performing MRI scans to screen all patients who have persistent back pain and received steroids from one of three contaminated batches. Previously, it advised scanning just those with new or worsening pain.

“People could be walking around with infections and they do not know it,’’ said Dr. Varsha Moudgal, head of infectious disease at St. Joseph ­Mercy Hospital in Ann Arbor, Mich., where Adair was hospitalized. “If they are untreated, they will cause pressure and damage to the spinal cord, and the concern then is about losing function.’’

Doctors at St. Joseph Mercy are scanning every patient with routine back pain who received a contaminated injection and have discovered infections among 14 percent of them. Among patients with new or worsening pain in Michigan, Tennessee, and North Carolina, MRIs have turned up infections in more than half. Since Nov. 29 alone, states have reported to the CDC at least 90 cases of ­spinal infections in patients who have not had meningitis.

The unexpected back infections add another element of worry for the nearly 14,000 ­patients across the country who received steroids laced with black mold from New England Compounding Center, amid what has been a trying 2½ months for many of them. While 39 patients have died, another 555 who have back ­infections, meningitis, or both, are facing an uncertain future. Many have relapsed and been hospitalized two or three times. Most have suffered debilitating side effects from antifungal drugs, including hallucinations.

At St. Joseph Mercy, where 30 patients are still hospitalized with meningitis or spinal infections, several patients have significant kidney damage caused by amphotericin, the drug Adair received during her third hospital stay. Even those who have gone home must undergo regular blood tests, electrocardiograms, MRIs, and painful spinal taps so doctors can closely monitor their condition.

Particularly distressing is that doctors do not know how long patients will require medication — estimates range from three months to a year — and whether the drugs will ultimately eliminate the fungus from their bodies, said a dozen patients, attorneys, and infectious disease specialists interviewed by the Globe.

Dr. John Perfect of Duke University Medical Center, a leading fungal disease specialist, said the medical profession “is flying by the seat” of its pants.

At the same time, investigators from the CDC and Food and Drug Administration are still searching for firm answers to basic questions about why the outbreak has progressed the way it has: Why did some states, such as Michigan and Tennessee, see a higher percentage of patients given the contaminated steroids get sick? And why is the number of ­patients with spinal infections still growing?

“The doctor has been really honest,’’ said Michael Mullins of High Point, N.C., who was diagnosed with meningitis on Oct. 5 and now has two small spinal abscesses. “We know meningitis can kind of linger. You can get sick later on in life. Whether this fungal meningitis will do this we don’t know. The only people who have lived through this kind of thing are those who are here now.’’

Adair, called Penny by her family and friends, had her first steroid injection from a contaminated batch Aug. 16 at a pain clinic near her home in ­rural South Lyon, about 20 miles north of Ann Arbor. She experienced terrible pain for weeks afterward, but doctors believed it was due to her ­degenerative disc disease, and she had a second contaminated steroid injection on Sept. 17.

By mid-October, Adair was in too much discomfort to walk, and her husband, a machine builder, drove her to the emergency room. It was the first of 41 days she would spend in the hospital during three stays, includ­ing Thanksgiving and her 50th birthday; they had planned to celebrate with a backyard bonfire and cookout.

Like many patients in the early days of the outbreak, Adair was initially misdiagnosed, with a pinched nerve, because her spinal fluid tested negative for meningitis. It was not until her second stay that doctors performed an MRI scan and found the abscess, she said. They put the mother of two on an antifungal drug called ­voriconazole and told her she would need a walker.

After Adair’s husband wheeled her into the emergency room
Nov. 15, doctors realized the infection was eating away her vertebrae. She teared up when they told her they would have to operate to drain fluid, scrape away infected portions of bone, and remove part of a disc.

“If the fungus is allowed to grow and thrive, it will infect the nerves in the spine, and that has far more ominous implications for patients,’’ said Dr. Douglas Geiger, a neuro­surgeon at St. Joseph Mercy.

After the surgery, doctors pumped a stronger and more toxic antifungal drug, amphotericin, into Adair’s body, but had to temporarily stop the lemon-colored intravenous drip because she was showing signs of kidney damage. “I had never been so scared in my life as when I thought it was attacking my kidneys,” she said. “I almost refused this treatment at the very end.’’

Michigan doctors have grown particularly aggressive about screening and treating patients, in part because the state received steroids from a batch they are calling a “hot lot’’ that appears to be more highly contaminated. Like Adair, most patients in the state received contaminated injections at Michigan Pain Specialists in Brighton, which got 400 vials of methylpredisolone acetate from lot 06292012@26, made by New England Compounding pharmacists in June.

Tennessee health officials have found that patients injected with the steroid from this lot were four times as likely to ­develop fungal disease as those injected with steroids from the other two implicated lots. More fungus could have gotten into this lot during mixing at New England Compounding, or it could have sat on shelves longer, giving the mold more time to grow, doctors said.

This lot might be one reason why a greater percentage of ­patients in Michigan got sick, or it could be that pain specialists there injected steroids in a way that made it easier for the fungus to take root and spread, Dr. John Jernigan of the CDC said in an interview. As to why the number of spinal infections is growing, specialists theorize that the incubation period could be longer than for meningitis or that it has taken longer for patients and doctors to recognize and report infections.

Adair is now at home, taking antifungal pills and waiting for her incision to heal. She requires morphine to get out of bed in the morning, but doctors have told her the pain should subside as her back heals. She has put breeding dogs and chickens, and tending her flower and vegetable gardens, on hold. Her husband, who depends on overtime to help make ends meet, did not get any extra pay last month while he helped care for her. They missed a mortgage payment and are working with the bank.

“We are just lucky I didn’t die,’’ Adair said. “I just don’t want to lose my house over this.”

Many of the patients stricken with meningitis early on are still dealing with the physical and emotional fallout from their disease.

Virginia Milne, 65, developed meningitis while traveling with her family in Europe, and after 31 days in the hospital, she is now home coping with the side effects of treatment. Milne got a steroid injection in her lower back Sept. 5 because she did not want her chronic back pain to ruin the trip. By the time she arrived in London two weeks later, she had developed a terrible headache.

Her husband wanted to ­return home to Virginia, but Milne insisted they go on to ­Ireland to meet a cousin. There she ended up in a small rural hospital, but they had not heard about the fungal meningitis outbreak in the United States, so she was not diagnosed until she got back. At one point, amphotericin caused such serious side effects — acute kidney failure and fluid in her lungs — that doctors pulled her off the medication.

“Late at night when there was no one there to talk to I would think, maybe this is how multiple organ failure occurs,” she said.

Now, side effects from a different drug include trouble concentrating, an unsettled stomach, swollen feet and ­ankles, and hand tremors.

“My doctors are not willing to say it’s the drug and it will get better,’’ she said.